Critique
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This paper describes a study that used a computational tool called CMfinder to search for structured non-coding RNAs (ncRNAs) in vertebrate genomes within ENCODE regions. CMfinder identified over 6,500 candidate ncRNA regions with an estimated false positive rate of 50%. A subset of 11 candidates were experimentally verified, with 10 shown to be present as RNA transcripts in specific tissues. The study found that considering RNA secondary structure, as CMfinder does, can help identify ncRNAs that may be missed by sequence-based alignment methods alone. The study also discussed some of the challenges in accurately identifying ncRNAs computationally.
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![Paper Critique Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions Amer Talal Wazwaz [email_address] [email_address] 18/4/2011](https://image.slidesharecdn.com/critique-110529094539-phpapp02/85/Critique-1-320.jpg)
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COMPETENCY 3Integrate credible and relevant sources into coursew
COMPETENCY 3
Integrate credible and relevant sources into coursework to enhance clarity and support claims.
CRITERION
Reflect on how credibility and relevance of a chosen resource were determined.
Your result: Non-Performance
Distinguished
Reflects on how credibility and relevance of a chosen resource were determined. Notes how specific aspects of the assessment were used to determine relevance.
Proficient
Reflects on how credibility and relevance of a chosen resource were determined.
Basic
Explains the concepts of credibility and relevance in general terms, but does not specifically address how this was used to determine if the specific resource was credible and relevant.
Non-Performance
Does not explain the concepts of credibility and relevance in general terms.
Faculty Comments:
I did not see a discussion of source credibility/relevance. For this assignment you were are also required to locate an article in the library about time organizing strategies (outlined in Part I). Then, you were asked in Part II to reflect on how you determined the credibility and relevance of your chosen library resource to support your task prioritization.
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Abstract. Numerous types of molecular mechanisms mediate
the development of cancer. Non-coding RNAs (ncRNAs) are
being increasingly recognized to play important role in medi-
ating the development of diseases, including cancer. Long
non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are
the two most widely studied ncRNAs. Thus far, lncRNAs are
known to have biological roles through a variety of mecha-
nisms, including genetic imprinting, chromatin remodeling,
cell cycle control, splicing regulation, mRNA decay and
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RNA, the mechanisms underlying the physiological or patho-
logical processes mediated by various types of ncRNAs, and
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1) The document discusses a study analyzing the impact of gene length on detecting differentially expressed genes using RNA-seq technology.
2) The study will first test the reproducibility of RNA-seq and the effect of normalization. It will then compare different statistical tests for identifying differentially expressed genes.
3) Finally, the study will specifically test how gene length impacts the likelihood of a gene being identified as differentially expressed, as longer genes are easier to map with short reads.
Transcriptome analysis
The document provides an overview of the history and techniques of transcriptome analysis. It discusses how RNA was separated from DNA with the formulation of the central dogma in 1958. Key developments include the discoveries of messenger RNA, transfer RNA, and ribosomal RNA in the 1960s. The document outlines techniques such as serial analysis of gene expression (SAGE) and RNA sequencing (RNA-seq) that allow comprehensive analysis of gene expression patterns. It provides details on the basic steps and advantages of SAGE and describes how next generation sequencing revolutionized transcriptome analysis through massive parallel sequencing.
BTC 810 Analysis of Transcriptomes.pptx
The document provides a history of transcriptomics and an overview of RNA analysis techniques. It begins by explaining Francis Crick's central dogma and the discovery of messenger RNA, transfer RNA, and ribosomal RNA in the 1960s. Later developments include the discoveries of RNA splicing, ribozymes, RNA interference, and small interfering RNA. The document then defines the transcriptome and describes methods for analyzing RNA expression like transcript formation, RNA structure, positional integration on the transcriptome, Northern blotting, serial analysis of gene expression (SAGE), and the basic steps of SAGE.
31931 31941
This document provides an overview of Serial Analysis of Gene Expression (SAGE). SAGE allows for the digital analysis of overall gene expression patterns in a sample by producing a snapshot of the mRNA population. It provides a quantitative and comprehensive expression profile. The document outlines the key principles and steps of the SAGE methodology, including isolating mRNA, synthesizing cDNA, ligating linkers, releasing tags, concatenating tags, and sequencing. It also discusses various applications and advances of SAGE, such as LongSAGE, CAGE, and SuperSAGE. SAGE is a powerful tool for studying gene expression, but it has some limitations regarding transcript identification and quantitation bias.
International Journal of Engineering Research and Development
This document discusses a study that uses the ke-REM (ke-Rule Extraction Method) classifier to predict promoter regions in DNA sequences. The study evaluates the performance of ke-REM compared to existing promoter prediction techniques. ke-REM constructs rules based on attribute-value pairs from a dataset of 106 E. coli DNA sequences, each containing 57 nucleotides. The results show that ke-REM competes well with existing methods for identifying promoter regions in DNA.
Rna seq and chip seq
This document provides an overview of RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq). It describes that RNA-Seq is used to profile transcriptomes and determine gene expression levels, while ChIP-Seq identifies the binding sites of DNA-associated proteins. The key steps of RNA-Seq are RNA preparation, library preparation, sequencing, and analysis to map reads, detect isoforms and expression levels. ChIP-Seq combines chromatin immunoprecipitation with sequencing to precisely map global binding sites of proteins of interest to understand gene regulation. Both techniques provide high-quality, genome-wide data with low input requirements compared to previous methods.
Sequence alignment
This document discusses sequence alignment, which involves arranging biological sequences like DNA, RNA, or proteins to identify regions of similarity. It covers the basic concepts of sequence alignment including global versus local alignment and different methods like dot matrix, dynamic programming, and word-based approaches. Dynamic programming is highlighted as the most common algorithm that uses a scoring system to find the optimal alignment between two sequences.
DNA Sequencing in Phylogeny
This document discusses DNA sequencing and phylogenetic analysis. It defines DNA sequencing as determining the order of nucleotide bases in a DNA molecule. It describes several DNA sequencing techniques like Sanger sequencing and nanopore sequencing. It explains how DNA sequencing results are used to infer phylogenetic relationships and construct phylogenetic trees showing evolutionary relationships among species. It discusses applications of DNA sequencing and phylogenetic analysis in fields like medicine, forensics, and tracing pathogen evolution.
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More from Amer T. Wazwaz
Amer MBT's Defense
This document summarizes a study on silencing the Elongation factor 1-alpha (EF1α) gene in Tomato yellow leaf curl virus (TYLCV)-resistant tomato plants. The objectives were to silence EF1α and observe if resistance collapsed. Results showed that after silencing EF1α in resistant plants and inoculating with TYLCV, the resistance collapsed, as seen in increased virus infection and symptoms matching susceptible plants. It was concluded that EF1α is important for TYLCV resistance. Further study of EF1α's role in the resistance gene network was recommended.
Gene silencing assaf's paper
This document describes a study that used virus-induced gene silencing (VIGS) to investigate the role of the hexose transporter gene LeHT1 in tomato resistance to Tomato yellow leaf curl virus (TYLCV). The gene was silenced in resistant and susceptible tomato lines. Silencing LeHT1 compromised resistance in resistant plants, allowing higher virus accumulation. Silenced resistant plants also developed necrosis and oxidative burst symptoms in response to TYLCV and other viruses. The results suggest LeHT1 plays a role in resistance by limiting virus entry/movement in cells and that silencing uncovered a secondary resistance mechanism involving programmed cell death.
Micro rn as gene silencing prez
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression in eukaryotes by binding to messenger RNA (mRNA) transcripts. MiRNAs undergo a complex biogenesis process, where they are processed from pri-miRNA to pre-miRNA and finally to a mature miRNA incorporated into an RNA-induced silencing complex (RISC). As part of RISC, miRNAs guide mRNA cleavage or translational repression of target genes by binding to partially complementary sites. This miRNA-mediated gene silencing plays important roles in diverse biological processes such as development, differentiation, and metabolism.
Tylcv seminar
This document summarizes a study that used virus-induced gene silencing (VIGS) to identify host genes involved in Tomato yellow leaf curl virus (TYLCV) infection of Nicotiana benthamiana plants. Researchers screened 54 candidate host genes and found that silencing 18 of them altered TYLCV infection based on effects on GFP expression patterns. Silencing of 7 genes had an antiviral effect by reducing viral DNA accumulation, while silencing of 11 other genes promoted infection by increasing viral DNA levels. Most notably, silencing of the deltaCOP subunit completely abolished TYLCV accumulation.
Post glactial colonization
1) This study analyzed genetic data from 369 Norway spruce populations to infer glacial refugia and postglacial colonization routes.
2) Genetic groups identified through SAMOVA and PCA clustering were compared to fossil pollen data, showing Norway spruce survived in at least seven refugial areas and expanded during the Holocene.
3) Within-population diversity was unexpectedly low in some refugial areas but high in most regions of early expansion, demonstrating the influence of glacial cycles and demographic changes on genetic variation.
Speciation prez
This study compared biodiversity between Eastern Asia and Eastern North America by analyzing 10 plant genera with sister clades in each region. For 7 of the 10 pairs, the Eastern Asian clade had longer branch lengths, indicating faster molecular evolution, and more species. Regression analysis found a positive relationship between molecular evolution rate and species richness. The results provide evidence that higher rates of molecular evolution in Eastern Asia may have led to more rapid speciation, contributing to its greater plant diversity compared to Eastern North America.
Anther culture
This study investigated factors affecting microspore-derived embryo formation in broccoli. The results showed that a 0.5X strength NLN liquid medium with 13% sucrose and a 24 hour heat shock treatment at 32.5°C produced the highest microspore-derived embryo yields. Higher concentrations of nutrients or sucrose inhibited embryo formation, while lower concentrations did not support microspore survival and division. These parameters provide an optimized protocol for microspore culture in broccoli.
Bacterial contaminants of plant tissue culture
This document discusses bacterial contaminants in plant tissue culture and methods for controlling contamination. It notes that the culture medium provides nutrients for bacteria and stressed plant tissues can be susceptible to infection. Contaminants may originate from explants, operators, or ineffective sterilization. Procedures to produce aseptic cultures require identifying and characterizing contaminants and eliminating them using improved practices, antibiotics, or other agents. Modern identification techniques include Biolog, API, fatty acid analysis, and 16S rRNA analysis. Common contaminants and effective antibiotic treatments are also discussed.
Functional and physical interaction between srk2 e and abi1
1. The document discusses the activation of the SnRK2 protein SRK2E/OST1 by abscisic acid (ABA) and low humidity stress.
2. It examines the roles of the phosphatases ABI1 and ABI2 in regulating SRK2E/OST1 under ABA signaling and in response to water loss.
3. The C-terminal domain of SRK2E/OST1 is found to physically interact with ABI1, and this interaction plays a critical role in controlling stomatal closure in response to ABA and low humidity stress.
Chromatin
1st ChIP-SAGE uses ChIP to purify chromatin, then crosslinks are reversed and linkers are ligated to DNA ends before digestion with NlaIII and MmeI to produce 21-22 bp sequence tags for cloning and sequencing.
2nd Deposition of histone variants like H2A.Z and H3.3 mark boundaries of regulatory regions in genomes and create hierarchical nucleosome stability.
3rd Interpreting ChIP experiments requires considering antibody specificity, chromatin preparation methods, and that results reflect average modification states across cells.
Genomics' prez 1
Consanguineous marriages can increase susceptibility to infectious diseases like tuberculosis and hepatitis B. A study found strong associations between consanguinity and susceptibility to TB and hepatitis B in West African populations with high rates of cousin marriages. However, there was no significant association found for hepatitis B in Italians, who have low cousin marriage rates, or for leprosy in Indians. The level of inbreeding appears to influence susceptibility, as first-cousin marriages were necessary to account for observed susceptibility levels in Gambia. Managing consanguinity risks requires social awareness programs, population genetic screening, youth counseling, and warning those at high risk.
Cataloging computationally putative resistance genes in grape and
1. The document discusses a bioinformatics project to catalog computationally putative resistance genes in grape and their corresponding pathogenicity genes.
2. The project searches databases to find main pathogenicity genes in pathogens and resistance genes in Arabidopsis thaliana, then catalogs them and uses BLAST to search for matches in grape genomes.
3. Examples show matches found between the rpfF gene in Xylella fastidiosa and the virB2 gene in Agrobacterium tumefaciens when BLASTed against grape genomes.
Ensembl genome
Ensembl Genomes is a portal that provides integrated access to genome-scale data for non-vertebrate species. It was developed using the Ensembl genome annotation and visualization platform. It consists of sub-portals for bacteria, protists, fungi, plants and invertebrate metazoa that complement the vertebrate genomes available in Ensembl. It provides graphical views of genomes and genes using the Ensembl genome browser software. Data is retrieved through interfaces like BioMart and APIs that access relational databases describing genomic features, sequences and identifiers. Tools like the Assembly Converter and Variant Effect Predictor are also available.
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Critique
- 1. Paper Critique Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions Amer Talal Wazwaz [email_address] [email_address] 18/4/2011